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<A HREF="#_A_">A</A> <A HREF="#_B_">B</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_F_">F</A> <A HREF="#_G_">G</A> <A HREF="#_H_">H</A> <A HREF="#_I_">I</A> <A HREF="#_K_">K</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_O_">O</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_V_">V</A> <A HREF="#_W_">W</A> <HR>
<A NAME="_A_"><!-- --></A><H2>
<B>A</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html#add(java.lang.String)"><B>add(String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.HashMapKeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html#add(java.lang.String)"><B>add(String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.KeywordTree</A>
<DD>Add a string to the keyword tree.
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#appendReplacement(java.lang.StringBuffer, java.lang.String)"><B>appendReplacement(StringBuffer, String)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#appendTail(java.lang.StringBuffer)"><B>appendTail(StringBuffer)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_B_"><!-- --></A><H2>
<B>B</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html#beginningChars()"><B>beginningChars()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.KeywordTree</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_C_"><!-- --></A><H2>
<B>C</B></H2>
<DL>
<DT><A HREF="./com/google/code/regexp/package-summary.html"><B>com.google.code.regexp</B></A> - package com.google.code.regexp<DD>&nbsp;<DT><A HREF="./de/hu/wbi/histoner/StringlengthComparator.html#compare(java.lang.String, java.lang.String)"><B>compare(String, String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/StringlengthComparator.html" title="class in de.hu.wbi.histoner">StringlengthComparator</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#compareTo(de.hu.wbi.histoner.HistoneModification)"><B>compareTo(HistoneModification)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/Span.html#compareTo(de.hu.wbi.histoner.train.Span)"><B>compareTo(Span)</B></A> - 
Method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/Span.html" title="class in de.hu.wbi.histoner.train">Span</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#compile(java.lang.String, int, java.lang.String)"><B>compile(String, int, String)</B></A> - 
Static method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html#containsPrefix(java.lang.String)"><B>containsPrefix(String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.HashMapKeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html#containsPrefix(java.lang.String)"><B>containsPrefix(String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.KeywordTree</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_D_"><!-- --></A><H2>
<B>D</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/package-summary.html"><B>de.hu.wbi.histoner</B></A> - package de.hu.wbi.histoner<DD>HistoNer is a high-performance, named entity recognition library for histone modifications 
 This package contains all code required to run HistoNer<DT><A HREF="./de/hu/wbi/histoner/eval/package-summary.html"><B>de.hu.wbi.histoner.eval</B></A> - package de.hu.wbi.histoner.eval<DD>This package contains all the code required to evaluate Histoner<DT><A HREF="./de/hu/wbi/histoner/train/package-summary.html"><B>de.hu.wbi.histoner.train</B></A> - package de.hu.wbi.histoner.train<DD>This package contains the relevant code to generate pattern for HistoNer</DL>
<HR>
<A NAME="_E_"><!-- --></A><H2>
<B>E</B></H2>
<DL>
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#end()"><B>end()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#end(int)"><B>end(int)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#end(java.lang.String)"><B>end(String)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatchResult.html#end(java.lang.String)"><B>end(String)</B></A> - 
Method in interface com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatchResult.html" title="interface in com.google.code.regexp">NamedMatchResult</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#equals(java.lang.Object)"><B>equals(Object)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/eval/Evaluate.html" title="class in de.hu.wbi.histoner.eval"><B>Evaluate</B></A> - Class in <A HREF="./de/hu/wbi/histoner/eval/package-summary.html">de.hu.wbi.histoner.eval</A><DD>Compare predictions of HistoNer against the manually annotated gold standard<DT><A HREF="./de/hu/wbi/histoner/eval/Evaluate.html#Evaluate()"><B>Evaluate()</B></A> - 
Constructor for class de.hu.wbi.histoner.eval.<A HREF="./de/hu/wbi/histoner/eval/Evaluate.html" title="class in de.hu.wbi.histoner.eval">Evaluate</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/Example.html" title="class in de.hu.wbi.histoner"><B>Example</B></A> - Class in <A HREF="./de/hu/wbi/histoner/package-summary.html">de.hu.wbi.histoner</A><DD>Minimal example for named entity recognition of histone modifications<DT><A HREF="./de/hu/wbi/histoner/Example.html#Example()"><B>Example()</B></A> - 
Constructor for class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/Example.html" title="class in de.hu.wbi.histoner">Example</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoNER.html#extractHistoneModifications(java.lang.String)"><B>extractHistoneModifications(String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoNER.html" title="class in de.hu.wbi.histoner">HistoNER</A>
<DD>Core of HistoNer:
 Searches and normalizes histone modifciations to Brno-nomenclature
</DL>
<HR>
<A NAME="_F_"><!-- --></A><H2>
<B>F</B></H2>
<DL>
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#find()"><B>find()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#find(int)"><B>find(int)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#flags()"><B>flags()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_G_"><!-- --></A><H2>
<B>G</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#getAaposition()"><B>getAaposition()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/Span.html#getEnd()"><B>getEnd()</B></A> - 
Method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/Span.html" title="class in de.hu.wbi.histoner.train">Span</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#getEntity()"><B>getEntity()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#getFrom()"><B>getFrom()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#getHistone()"><B>getHistone()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#getId()"><B>getId()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#getModification()"><B>getModification()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#getModificationRegex()"><B>getModificationRegex()</B></A> - 
Static method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>Builds a regular expression string consisting of all different modification terms.
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#getPatternId()"><B>getPatternId()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html#getPrefixes()"><B>getPrefixes()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.HashMapKeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html#getPrefixes()"><B>getPrefixes()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.KeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#getResidue()"><B>getResidue()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/Span.html#getStart()"><B>getStart()</B></A> - 
Method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/Span.html" title="class in de.hu.wbi.histoner.train">Span</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html#getSubTree(java.lang.String)"><B>getSubTree(String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.HashMapKeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html#getSubTree(java.lang.String)"><B>getSubTree(String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.KeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#getTo()"><B>getTo()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#group()"><B>group()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#group(int)"><B>group(int)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#group(java.lang.String)"><B>group(String)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatchResult.html#group(java.lang.String)"><B>group(String)</B></A> - 
Method in interface com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatchResult.html" title="interface in com.google.code.regexp">NamedMatchResult</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#groupCount()"><B>groupCount()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#groupNames()"><B>groupNames()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_H_"><!-- --></A><H2>
<B>H</B></H2>
<DL>
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#hasAnchoringBounds()"><B>hasAnchoringBounds()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#hashCode()"><B>hashCode()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#hashCode()"><B>hashCode()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#hasTransparentBounds()"><B>hasTransparentBounds()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner"><B>HistoneModification</B></A> - Class in <A HREF="./de/hu/wbi/histoner/package-summary.html">de.hu.wbi.histoner</A><DD>Represents a histone - modification; a histone modification consists of 
 
  Histone number (1, 2A, 2B, 3, 3.3, 4, 5)
  Amino acid (Lysine, Arginine, Serine, Threonine and Glutamate) 
  Position of the amino acid modification 
  The modification itself (methylation, acetylation, etc.)<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#HistoneModification(java.lang.String, java.lang.String, de.hu.wbi.histoner.HistoneModification.Residue, int, int, int, java.lang.String)"><B>HistoneModification(String, String, HistoneModification.Residue, int, int, int, String)</B></A> - 
Constructor for class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>Creates a histone modification
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#HistoneModification(java.lang.String)"><B>HistoneModification(String)</B></A> - 
Constructor for class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>Creates a histone modification  from a string following the Brno nomenclature
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner"><B>HistoneModification.Residue</B></A> - Enum in <A HREF="./de/hu/wbi/histoner/package-summary.html">de.hu.wbi.histoner</A><DD>Represents an amino acid<DT><A HREF="./de/hu/wbi/histoner/HistoNER.html" title="class in de.hu.wbi.histoner"><B>HistoNER</B></A> - Class in <A HREF="./de/hu/wbi/histoner/package-summary.html">de.hu.wbi.histoner</A><DD>Named entity recognition for histone modifications<DT><A HREF="./de/hu/wbi/histoner/HistoNER.html#HistoNER(java.lang.String)"><B>HistoNER(String)</B></A> - 
Constructor for class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoNER.html" title="class in de.hu.wbi.histoner">HistoNER</A>
<DD>Constructor with supplied regexFile
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#hitEnd()"><B>hitEnd()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_I_"><!-- --></A><H2>
<B>I</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html#in"><B>in</B></A> - 
Static variable in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html" title="class in de.hu.wbi.histoner.train">PatternBootstrap</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/RawPatternGenerator.html#input"><B>input</B></A> - 
Static variable in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/RawPatternGenerator.html" title="class in de.hu.wbi.histoner.train">RawPatternGenerator</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html#isDollar()"><B>isDollar()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.HashMapKeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html#isDollar()"><B>isDollar()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.KeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html#isEmpty()"><B>isEmpty()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.HashMapKeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html#isEmpty()"><B>isEmpty()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.KeywordTree</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_K_"><!-- --></A><H2>
<B>K</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.html#keywordTreeToRegex(de.hu.wbi.histoner.OptionalRegexOptimizer.KeywordTree)"><B>keywordTreeToRegex(OptionalRegexOptimizer.KeywordTree)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_L_"><!-- --></A><H2>
<B>L</B></H2>
<DL>
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#lookingAt()"><B>lookingAt()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_M_"><!-- --></A><H2>
<B>M</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/eval/Evaluate.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.wbi.histoner.eval.<A HREF="./de/hu/wbi/histoner/eval/Evaluate.html" title="class in de.hu.wbi.histoner.eval">Evaluate</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/eval/Predict.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.wbi.histoner.eval.<A HREF="./de/hu/wbi/histoner/eval/Predict.html" title="class in de.hu.wbi.histoner.eval">Predict</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/Example.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/Example.html" title="class in de.hu.wbi.histoner">Example</A>
<DD>Minimal example for running HistoNer on free text
<DT><A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html" title="class in de.hu.wbi.histoner.train">PatternBootstrap</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/RawPatternGenerator.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/RawPatternGenerator.html" title="class in de.hu.wbi.histoner.train">RawPatternGenerator</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/RegexOptimizer.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/RegexOptimizer.html" title="class in de.hu.wbi.histoner.train">RegexOptimizer</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/Sentences.html#main(java.lang.String[])"><B>main(String[])</B></A> - 
Static method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/Sentences.html" title="class in de.hu.wbi.histoner.train">Sentences</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#matcher(java.lang.CharSequence)"><B>matcher(CharSequence)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#matches()"><B>matches()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_N_"><!-- --></A><H2>
<B>N</B></H2>
<DL>
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#namedGroups()"><B>namedGroups()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatchResult.html#namedGroups()"><B>namedGroups()</B></A> - 
Method in interface com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatchResult.html" title="interface in com.google.code.regexp">NamedMatchResult</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp"><B>NamedMatcher</B></A> - Class in <A HREF="./com/google/code/regexp/package-summary.html">com.google.code.regexp</A><DD>&nbsp;<DT><A HREF="./com/google/code/regexp/NamedMatchResult.html" title="interface in com.google.code.regexp"><B>NamedMatchResult</B></A> - Interface in <A HREF="./com/google/code/regexp/package-summary.html">com.google.code.regexp</A><DD>&nbsp;<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#namedPattern()"><B>namedPattern()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp"><B>NamedPattern</B></A> - Class in <A HREF="./com/google/code/regexp/package-summary.html">com.google.code.regexp</A><DD>&nbsp;<DT><A HREF="./com/google/code/regexp/NamedPattern.html#namedPattern()"><B>namedPattern()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html#nToken"><B>nToken</B></A> - 
Static variable in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html" title="class in de.hu.wbi.histoner.train">PatternBootstrap</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_O_"><!-- --></A><H2>
<B>O</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.html#optimize(java.lang.String)"><B>optimize(String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer</A>
<DD>Optimizes a regular expression
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.html" title="class in de.hu.wbi.histoner"><B>OptionalRegexOptimizer</B></A> - Class in <A HREF="./de/hu/wbi/histoner/package-summary.html">de.hu.wbi.histoner</A><DD>Class used to optimize regular expressions for speed<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.html#OptionalRegexOptimizer()"><B>OptionalRegexOptimizer()</B></A> - 
Constructor for class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner"><B>OptionalRegexOptimizer.HashMapKeywordTree</B></A> - Class in <A HREF="./de/hu/wbi/histoner/package-summary.html">de.hu.wbi.histoner</A><DD>&nbsp;<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html#OptionalRegexOptimizer.HashMapKeywordTree()"><B>OptionalRegexOptimizer.HashMapKeywordTree()</B></A> - 
Constructor for class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.HashMapKeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html#OptionalRegexOptimizer.HashMapKeywordTree(int)"><B>OptionalRegexOptimizer.HashMapKeywordTree(int)</B></A> - 
Constructor for class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.HashMapKeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html" title="class in de.hu.wbi.histoner"><B>OptionalRegexOptimizer.KeywordTree</B></A> - Class in <A HREF="./de/hu/wbi/histoner/package-summary.html">de.hu.wbi.histoner</A><DD>&nbsp;<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html#OptionalRegexOptimizer.KeywordTree()"><B>OptionalRegexOptimizer.KeywordTree()</B></A> - 
Constructor for class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.KeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.KeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#orderedGroups()"><B>orderedGroups()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatchResult.html#orderedGroups()"><B>orderedGroups()</B></A> - 
Method in interface com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatchResult.html" title="interface in com.google.code.regexp">NamedMatchResult</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html#out"><B>out</B></A> - 
Static variable in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html" title="class in de.hu.wbi.histoner.train">PatternBootstrap</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/RawPatternGenerator.html#output"><B>output</B></A> - 
Static variable in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/RawPatternGenerator.html" title="class in de.hu.wbi.histoner.train">RawPatternGenerator</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#overlaps(de.hu.wbi.histoner.HistoneModification)"><B>overlaps(HistoneModification)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>Checks if two histone modifications do overlap.
</DL>
<HR>
<A NAME="_P_"><!-- --></A><H2>
<B>P</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html" title="class in de.hu.wbi.histoner.train"><B>PatternBootstrap</B></A> - Class in <A HREF="./de/hu/wbi/histoner/train/package-summary.html">de.hu.wbi.histoner.train</A><DD>Class can be used to bootstrap new pattern from the original (non-annotated) pattern file.<DT><A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html#PatternBootstrap()"><B>PatternBootstrap()</B></A> - 
Constructor for class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html" title="class in de.hu.wbi.histoner.train">PatternBootstrap</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/eval/Predict.html" title="class in de.hu.wbi.histoner.eval"><B>Predict</B></A> - Class in <A HREF="./de/hu/wbi/histoner/eval/package-summary.html">de.hu.wbi.histoner.eval</A><DD>Class is used for named entity recognition on the gold-standard data
 It simply recognizes and normalizes all histone modicications in the annotated data to the Brno nomenclature<DT><A HREF="./de/hu/wbi/histoner/eval/Predict.html#Predict()"><B>Predict()</B></A> - 
Constructor for class de.hu.wbi.histoner.eval.<A HREF="./de/hu/wbi/histoner/eval/Predict.html" title="class in de.hu.wbi.histoner.eval">Predict</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_R_"><!-- --></A><H2>
<B>R</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/train/RawPatternGenerator.html" title="class in de.hu.wbi.histoner.train"><B>RawPatternGenerator</B></A> - Class in <A HREF="./de/hu/wbi/histoner/train/package-summary.html">de.hu.wbi.histoner.train</A><DD>Class generates raw un-annotated pattern, by searching for modification terms, numbers, and amino acids from a file consisting of sentences.<DT><A HREF="./de/hu/wbi/histoner/train/RawPatternGenerator.html#RawPatternGenerator()"><B>RawPatternGenerator()</B></A> - 
Constructor for class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/RawPatternGenerator.html" title="class in de.hu.wbi.histoner.train">RawPatternGenerator</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/eval/Predict.html#readFile(java.io.File)"><B>readFile(File)</B></A> - 
Static method in class de.hu.wbi.histoner.eval.<A HREF="./de/hu/wbi/histoner/eval/Predict.html" title="class in de.hu.wbi.histoner.eval">Predict</A>
<DD>Reads the content of a file and returns the content..
<DT><A HREF="./de/hu/wbi/histoner/train/RegexOptimizer.html" title="class in de.hu.wbi.histoner.train"><B>RegexOptimizer</B></A> - Class in <A HREF="./de/hu/wbi/histoner/train/package-summary.html">de.hu.wbi.histoner.train</A><DD>This is a post-processing step to generalize pattern to improve recall.<DT><A HREF="./de/hu/wbi/histoner/train/RegexOptimizer.html#RegexOptimizer()"><B>RegexOptimizer()</B></A> - 
Constructor for class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/RegexOptimizer.html" title="class in de.hu.wbi.histoner.train">RegexOptimizer</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#region(int, int)"><B>region(int, int)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#regionEnd()"><B>regionEnd()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#regionStart()"><B>regionStart()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#replaceAll(java.lang.String)"><B>replaceAll(String)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#replaceFirst(java.lang.String)"><B>replaceFirst(String)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#requireEnd()"><B>requireEnd()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#reset()"><B>reset()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#reset(java.lang.CharSequence)"><B>reset(CharSequence)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#residueMapping()"><B>residueMapping()</B></A> - 
Static method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>Mapping from different amino acid descriptors to the FASTA - one letter format
</DL>
<HR>
<A NAME="_S_"><!-- --></A><H2>
<B>S</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/train/Sentences.html" title="class in de.hu.wbi.histoner.train"><B>Sentences</B></A> - Class in <A HREF="./de/hu/wbi/histoner/train/package-summary.html">de.hu.wbi.histoner.train</A><DD>HistoNer learns pattern from raw natural language sentences.<DT><A HREF="./de/hu/wbi/histoner/train/Sentences.html#Sentences()"><B>Sentences()</B></A> - 
Constructor for class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/Sentences.html" title="class in de.hu.wbi.histoner.train">Sentences</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/Span.html#setEnd(int)"><B>setEnd(int)</B></A> - 
Method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/Span.html" title="class in de.hu.wbi.histoner.train">Span</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#setId(java.lang.String)"><B>setId(String)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#setPatternId(java.lang.String)"><B>setPatternId(String)</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/Span.html#setStart(int)"><B>setStart(int)</B></A> - 
Method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/Span.html" title="class in de.hu.wbi.histoner.train">Span</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/Span.html" title="class in de.hu.wbi.histoner.train"><B>Span</B></A> - Class in <A HREF="./de/hu/wbi/histoner/train/package-summary.html">de.hu.wbi.histoner.train</A><DD>Span is used to store start and stop position of a regular expression match.<DT><A HREF="./de/hu/wbi/histoner/train/Span.html#Span(int, int)"><B>Span(int, int)</B></A> - 
Constructor for class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/Span.html" title="class in de.hu.wbi.histoner.train">Span</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#split(java.lang.CharSequence, int)"><B>split(CharSequence, int)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#split(java.lang.CharSequence)"><B>split(CharSequence)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#standardPattern()"><B>standardPattern()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#standardPattern()"><B>standardPattern()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#start()"><B>start()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#start(int)"><B>start(int)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#start(java.lang.String)"><B>start(String)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatchResult.html#start(java.lang.String)"><B>start(String)</B></A> - 
Method in interface com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatchResult.html" title="interface in com.google.code.regexp">NamedMatchResult</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/StringlengthComparator.html" title="class in de.hu.wbi.histoner"><B>StringlengthComparator</B></A> - Class in <A HREF="./de/hu/wbi/histoner/package-summary.html">de.hu.wbi.histoner</A><DD>Sort two strings by length<DT><A HREF="./de/hu/wbi/histoner/StringlengthComparator.html#StringlengthComparator()"><B>StringlengthComparator()</B></A> - 
Constructor for class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/StringlengthComparator.html" title="class in de.hu.wbi.histoner">StringlengthComparator</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_T_"><!-- --></A><H2>
<B>T</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#toBrnoString()"><B>toBrnoString()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#toMatchResult()"><B>toMatchResult()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#toString()"><B>toString()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedPattern.html#toString()"><B>toString()</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedPattern.html" title="class in com.google.code.regexp">NamedPattern</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.html" title="class in de.hu.wbi.histoner">HistoneModification</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/OptionalRegexOptimizer.HashMapKeywordTree.html" title="class in de.hu.wbi.histoner">OptionalRegexOptimizer.HashMapKeywordTree</A>
<DD>&nbsp;
<DT><A HREF="./de/hu/wbi/histoner/train/Span.html#toString()"><B>toString()</B></A> - 
Method in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/Span.html" title="class in de.hu.wbi.histoner.train">Span</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_U_"><!-- --></A><H2>
<B>U</B></H2>
<DL>
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#useAnchoringBounds(boolean)"><B>useAnchoringBounds(boolean)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#usePattern(com.google.code.regexp.NamedPattern)"><B>usePattern(NamedPattern)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
<DT><A HREF="./com/google/code/regexp/NamedMatcher.html#useTransparentBounds(boolean)"><B>useTransparentBounds(boolean)</B></A> - 
Method in class com.google.code.regexp.<A HREF="./com/google/code/regexp/NamedMatcher.html" title="class in com.google.code.regexp">NamedMatcher</A>
<DD>&nbsp;
</DL>
<HR>
<A NAME="_V_"><!-- --></A><H2>
<B>V</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.Residue.html#valueOf(java.lang.String)"><B>valueOf(String)</B></A> - 
Static method in enum de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner">HistoneModification.Residue</A>
<DD>Returns the enum constant of this type with the specified name.
<DT><A HREF="./de/hu/wbi/histoner/HistoneModification.Residue.html#values()"><B>values()</B></A> - 
Static method in enum de.hu.wbi.histoner.<A HREF="./de/hu/wbi/histoner/HistoneModification.Residue.html" title="enum in de.hu.wbi.histoner">HistoneModification.Residue</A>
<DD>Returns an array containing the constants of this enum type, in
the order they are declared.
</DL>
<HR>
<A NAME="_W_"><!-- --></A><H2>
<B>W</B></H2>
<DL>
<DT><A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html#whitespace"><B>whitespace</B></A> - 
Static variable in class de.hu.wbi.histoner.train.<A HREF="./de/hu/wbi/histoner/train/PatternBootstrap.html" title="class in de.hu.wbi.histoner.train">PatternBootstrap</A>
<DD>&nbsp;
</DL>
<HR>
<A HREF="#_A_">A</A> <A HREF="#_B_">B</A> <A HREF="#_C_">C</A> <A HREF="#_D_">D</A> <A HREF="#_E_">E</A> <A HREF="#_F_">F</A> <A HREF="#_G_">G</A> <A HREF="#_H_">H</A> <A HREF="#_I_">I</A> <A HREF="#_K_">K</A> <A HREF="#_L_">L</A> <A HREF="#_M_">M</A> <A HREF="#_N_">N</A> <A HREF="#_O_">O</A> <A HREF="#_P_">P</A> <A HREF="#_R_">R</A> <A HREF="#_S_">S</A> <A HREF="#_T_">T</A> <A HREF="#_U_">U</A> <A HREF="#_V_">V</A> <A HREF="#_W_">W</A> 

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